Contacts of the helix formed by residues 105 - 117 (chain A) in PDB entry 2RGZ
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ARG 105 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78A TYR* 3.8 21.1 - - + -
82A GLU* 2.7 12.4 + - - +
102A GLU 4.8 0.8 + - - -
103A LEU 2.8 28.5 + - - +
104A HIS* 1.3 78.4 + - - +
106A LYS* 1.3 53.3 + - - +
107A GLU 3.2 3.1 - - - -
108A ALA* 2.7 37.2 + - - +
109A LEU* 2.8 33.4 + - + +
157A TYR* 4.1 3.6 - - + -
160A ASP* 4.6 0.2 - - - +
185A GLN 3.3 8.3 + - - -
186A PHE* 2.6 48.0 + - + +
188A LEU 2.6 29.8 + - - -
189A PHE* 3.2 43.4 - - + +
190A GLU 5.0 0.4 - - - +
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Residues in contact with LYS 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A TYR* 3.5 28.4 + - + -
78A TYR* 5.1 1.7 - - - +
79A SER* 2.8 38.6 + - - +
82A GLU* 3.0 20.1 + - + +
83A GLU* 5.2 6.9 + - - +
104A HIS* 3.7 0.4 - - - +
105A ARG* 1.3 77.5 - - - +
107A GLU* 1.3 55.4 + - - +
109A LEU* 4.3 8.2 - - - +
110A THR* 2.7 44.9 + - - +
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Residues in contact with GLU 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A HIS* 5.1 5.2 + - + +
105A ARG 3.2 0.8 - - - -
106A LYS* 1.3 77.5 - - - +
108A ALA* 1.3 59.8 + - - +
110A THR* 4.2 4.9 - - - -
111A LYS* 3.1 47.8 + - + +
190A GLU* 5.3 3.6 - - - +
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Residues in contact with ALA 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A HIS 5.4 0.4 + - - +
105A ARG* 2.7 31.6 + - - +
107A GLU* 1.3 78.2 - - - +
109A LEU* 1.3 66.5 + - - +
110A THR 3.2 1.1 - - - -
111A LYS* 3.1 12.8 + - - +
112A ASP* 3.0 26.0 + - - -
185A GLN* 3.2 27.1 - - - +
186A PHE* 3.7 5.4 - - - -
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Residues in contact with LEU 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A THR* 3.7 25.1 - - + -
74A LEU* 4.1 11.4 - - + -
75A TYR* 3.8 32.8 - - + +
78A TYR* 4.3 15.5 - - + -
105A ARG* 2.8 36.2 + - + +
106A LYS* 4.2 3.8 - - - +
108A ALA* 1.3 72.1 - - - +
110A THR* 1.3 52.4 + - - +
112A ASP* 2.6 26.3 + - - +
113A MET* 2.6 21.8 + - + +
186A PHE* 3.3 50.3 - - + -
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Residues in contact with THR 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A TYR* 4.0 12.2 - - - -
106A LYS* 2.7 34.3 + - - +
107A GLU* 4.2 6.7 - - - +
109A LEU* 1.3 75.5 - - - +
111A LYS* 1.3 65.0 + - + +
113A MET* 3.1 10.8 + - - +
114A GLU* 3.0 41.8 + - - +
121A TRP* 4.6 15.7 + - + -
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Residues in contact with LYS 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A GLU* 3.1 41.0 + - + +
108A ALA* 3.1 9.4 + - - +
110A THR* 1.3 80.2 - - + +
112A ASP* 1.3 62.6 + - - +
114A GLU* 3.4 20.2 - - - +
115A TYR* 3.3 20.3 + - - +
185A GLN* 2.9 44.3 + - - +
190A GLU* 4.4 19.2 + - - -
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Residues in contact with ASP 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A THR* 4.4 13.9 - - + -
108A ALA 3.0 10.3 + - - +
109A LEU* 2.6 18.9 + - - +
111A LYS* 1.3 70.4 - - - +
113A MET* 1.3 62.8 + - - +
114A GLU 3.1 1.8 - - - -
115A TYR* 3.3 13.4 + - - +
116A PHE* 3.4 22.8 + - + -
183A GLY* 3.1 25.0 + - - +
184A THR* 3.5 1.6 - - - -
185A GLN* 2.7 28.3 + - - +
186A PHE* 2.6 41.4 + - - +
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Residues in contact with MET 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A THR* 3.8 24.5 - - + -
72A THR* 3.4 32.5 - - - +
75A TYR* 4.9 11.4 - - + -
109A LEU 2.6 22.1 + - - +
110A THR* 3.5 9.6 - - - +
112A ASP* 1.3 72.7 - - - +
114A GLU* 1.3 61.1 + - - +
116A PHE* 6.2 0.7 - - - -
117A PHE* 3.3 47.3 + - + +
118A GLY 3.4 0.2 + - - -
121A TRP* 3.3 57.0 - - + +
125A VAL* 4.1 11.9 - - + -
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Residues in contact with GLU 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A THR* 3.0 27.5 + - - +
111A LYS* 3.4 29.4 - - - +
112A ASP 3.1 0.2 - - - -
113A MET* 1.3 78.9 - - - +
115A TYR* 1.3 59.6 + - - +
118A GLY* 2.9 29.7 + - - +
119A GLU* 2.8 45.6 + - + +
121A TRP* 4.0 9.0 + - + -
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Residues in contact with TYR 115 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64A LYS* 6.3 0.4 - - - -
111A LYS 3.3 8.9 + - - +
112A ASP 3.3 8.5 + - - +
114A GLU* 1.3 82.5 - - - +
116A PHE* 1.3 73.7 + + - +
118A GLY* 4.4 1.4 + - - -
177A LEU* 4.1 16.3 - - + +
178A PRO* 3.4 23.3 - - + +
182A GLU* 3.3 38.6 - - + -
183A GLY* 3.4 26.5 - - - +
185A GLN* 5.7 1.8 - - - +
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Residues in contact with PHE 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A LYS* 4.3 29.6 - - + -
67A PHE* 3.5 35.0 - + - -
68A LYS* 3.8 33.5 + - + +
71A THR* 4.6 11.0 - - - -
112A ASP* 3.4 22.3 + - + +
113A MET* 5.5 0.9 - - - -
115A TYR* 1.3 87.8 - + - +
117A PHE* 1.3 68.4 + + + +
175A LEU* 4.8 0.7 - - + -
177A LEU* 3.9 26.0 - - + -
183A GLY* 3.4 34.8 - - - -
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Residues in contact with PHE 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A GLU* 5.6 1.6 - - - -
68A LYS* 3.4 62.1 - - + +
69A LEU* 5.4 3.6 - - + -
72A THR* 3.7 7.6 - - - -
113A MET* 3.3 42.7 + - + +
116A PHE* 1.3 82.8 - + + +
118A GLY* 1.3 56.4 + - - +
120A ASN* 2.5 24.6 + - - +
121A TRP* 3.2 23.8 - - + -
124A GLN* 4.0 33.3 + - + +
125A VAL* 5.8 4.7 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il